Fig. 3

a Proportion of expression variance explained by species (x-axis) and by organs (y-axis) for each of the 6283 orthologous genes (dots) using linear models. The dashed lines at y=2x and x=2y identify the genes in which species-explained variance is twofold greater than organ-explained variance, and in which tissue-explained variance is twofold greater than species-explained variance, respectively. We restricted to the genes for which either species or tissue explains at least 75 % of the variance (dashed line at x+y=0.75), and defined two sets of genes: genes whose expression varies considerably across species and little across tissues, SVGs (green), and genes whose expression varies considerably across tissues and little across species, TVGs (orange). b Box plot representing the distribution of the proportion of gene expression variance across organs (light yellow) or between human and each other species (dark yellow). When considering more evolutionarily distant species, the proportion of variance across organs decreases, while that between species increases. c Number of genes in distinct bins of proportional residual variance (histogram) and cumulative proportion of genes at increasing bins of proportional residual variance. Altogether, 75 % of orthologous genes have less than 35 % residual variance. d PCA based on the expression of TVGs only shows an organ-dominated arrangement of the samples in the space defined by the first two PCs. e PCA based on the expression of SVGs only shows a species-dominated arrangement of the samples in the space defined by the first two PCs. f Same as (a), with different color scale, which highlights the higher variance across organs of genes identified by the projection score [13] (black), compared to the rest of the genes (gray). PC principal component, PCA principal component analysis, SVG species-variable gene, TVG tissue-variable gene